I usually only nickname my main team, with a few exceptions. For my White, the theme I had was close friends of mine (for the main team, at least).
Zebstrika: Michele. Her favorite animal is the Zebra, so the moment I saw Blitzle I just had to name it after her.
Cinccino: Melissa. After deciding what my theme was going to be, I went ti my friend and asked if she liked Chinchillas. After she said she did, I decided to name it after her.
Reuniclus: Emily. Not too much of a reason, other than the fact that I wanted to call something Emily and Reuniclus was the only thing I wanted on my team that didn't have a name. xD;
Lilligant: Lucia. My Bellossom was named Lucia on my Soul Silver, so since Lilligant was kid of like Lucia I just thought it was appropriate.
Chandelure: Shannon. Inside joke among the band during high school was 'Shandelier' so when I saw it I had to name it after her.
Swanna: Alyssa. It just seemed to fit, and I actually have two close friends called Alyssa so it works.
I nicknamed a few other Pokemon, which were the Pokemon I used because I got my main team.
Timburr: Logs
Tepig: The Pig
Patrat: Timon
Pansage: Mufflers
Lillipup: Puppers
... Yeah. XD;